def call_debruijn_graph(self, windows, reads):
"""Helper function to call debruijn_graph module."""
windows_haplotypes = []
# Build and process de-Bruijn graph for each window.
for window in windows:
if window.end - window.start > self.config.ws_config.max_window_size:
continue
if not self.ref_reader.is_valid_interval(window):
continue
ref = self.ref_reader.bases(window)
# redacted
dbg_reads = [
read for read in reads
if ranges.ranges_overlap(window, utils.read_range(read))
]
with timer.Timer() as t:
graph = debruijn_graph.build(ref, dbg_reads,
self.config.dbg_config)
graph_building_time = t.GetDuration()
if not graph:
candidate_haplotypes = [ref]
else:
candidate_haplotypes = graph.candidate_haplotypes()
if candidate_haplotypes and candidate_haplotypes != [ref]:
candidate_haplotypes_info = realigner_pb2.CandidateHaplotypes(
span=window, haplotypes=candidate_haplotypes)
windows_haplotypes.append(candidate_haplotypes_info)
self.diagnostic_logger.log_graph_metrics(window, graph,
candidate_haplotypes,
graph_building_time)
return windows_haplotypes
def call_debruijn_graph(self, windows, reads):
"""Helper function to call debruijn_graph module."""
windows_haplotypes = []
# Build and process de-Bruijn graph for each window.
sam_reader = sam.InMemorySamReader(reads)
for window in windows:
if window.end - window.start > self.config.ws_config.max_window_size:
continue
if not self.ref_reader.is_valid(window):
continue
ref = self.ref_reader.query(window)
window_reads = list(sam_reader.query(window))
with timer.Timer() as t:
graph = debruijn_graph.build(ref, window_reads, self.config.dbg_config)
graph_building_time = t.GetDuration()
if not graph:
candidate_haplotypes = [ref]
else:
candidate_haplotypes = graph.candidate_haplotypes()
if candidate_haplotypes and candidate_haplotypes != [ref]:
candidate_haplotypes_info = realigner_pb2.CandidateHaplotypes(
span=window, haplotypes=candidate_haplotypes)
windows_haplotypes.append(candidate_haplotypes_info)
self.diagnostic_logger.log_graph_metrics(
window, graph, candidate_haplotypes, graph_building_time)
return windows_haplotypes
def testVacuous(self):
with timer.Timer() as t:
pass
print('Time consuming stuff took %f seconds.' % t.GetDuration())